Three people are now confirmed to have died after a fishing boat with five people onboard capsized near Port Lincoln on South Australia’s Eyre Peninsula late on Monday afternoon.

At 6:30am on Tuesday, police found a body in the water, then another at 9am, before a third was discovered at 2:15pm.

The boat overturned overnight around Spilsby Island, 45 kilometres east of Port Lincoln in the Spencer Gulf.

Two survivors — a 44-year-old man and a 13-year-old boy, both from the Adelaide suburb of Torrens Park — were found on a reef and winched to safety in the early hours of Tuesday morning.

Police found the upturned and damaged vessel at about 2am on Tuesday near Spilsby Island in Spencer Gulf. (ABC News: Jodie Hamilton)

The surviving pair were taken to hospital where they are being treated for non-life-threatening injuries including hypothermia.

Police were told by the pair that the boat was capsized by a wave at about 4pm on Monday.

Family raised the alarm at about 8:30pm on Monday when the boat failed to return from a fishing trip that morning.

Superintendent Paul Bahr said investigations into the circumstances that surrounded the incident would continue.

Paul Bahr says police are still investigating the circumstances. (ABC News: Jodie Hamilton)

“They were fishing near Spilsby Island when they were swamped by a wave, overturning the boat and throwing everyone into the water,” Superintendent Bahr said. 

“We’re still talking to the survivors, so we’re still trying to put that picture together in terms of how they ended up on the reef away from the boat.”

He said a police helicopter located the upturned fishing boat at about 2am on Tuesday.

“The boat itself has also been recovered and it’s making its way back to Port Lincoln and that will be offloaded later today,” he said. 

“It will be subject to further forensic examination and also any examination the coroner may require.”

Aerial and ocean searches underway on Tuesday have now concluded. 

In a statement, SAPOL said it will prepare a report for the coroner. 

Posted , updated